COVID-19 plasma proteome reveals novel temporal and cell-specific signatures for disease severity and high-precision disease management

Coronavirus disease 2019 (COVID-19) is a systemic inflammatory condition with high mortality that may benefit from personalized medicine and high-precision approaches. COVID-19 patient plasma was analysed with targeted proteomics of 1161 proteins. Patients were monitored from Days 1 to 10 of their intensive care unit (ICU) stay. Age- and gender-matched COVID-19-negative sepsis ICU patients and healthy subjects were examined as controls. Proteomic data were resolved using both cell-specific annotation and deep-analysis for functional enrichment. COVID-19 caused extensive remodelling of the plasma microenvironment associated with a relative immunosuppressive milieu between ICU Days 3–7, and characterized by extensive organ damage. COVID-19 resulted in (1) reduced antigen presentation and B/T-cell function, (2) increased repurposed neutrophils and M1-type macrophages, (3) relatively immature or disrupted endothelia and fibroblasts with a defined secretome, and (4) reactive myeloid lines. Extracellular matrix changes identified in COVID-19 plasma could represent impaired immune cell homing and programmed cell death. The major functional modules disrupted in COVID-19 were exaggerated in patients with fatal outcome. Taken together, these findings provide systems-level insight into the mechanisms of COVID-19 inflammation and identify potential prognostic biomarkers. Therapeutic strategies could be tailored to the immune response of severely ill patients.     

Purification of human leucocyte DNA: proteinase K is not necessary.

A rapid nontoxic method for the purification of DNA from human leucocytes is described. Preliminary experiments which tested different methods of DNA purification indicated that digestion of proteins with proteinase K was unnecessary. This led to the development of a simple procedure involving lysis of the cells in SDS followed by extraction with 6 M NaCl. The method described overcomes the requirement for lengthy incubations in the presence of expensive proteinase K and subsequent extraction with toxic chemicals.     

RECURRENT FORMATION AND POLYPHYLY OF NORDIC POLYPLOIDS IN DRABA (BRASSICACEAE)

Draba (Brassicaceae) is well known for its taxonomic complexity in arctic and alpine floras, and the polyploids in particular present vexing taxonomic problems. It has been suggested that polyploids in Draba may have formed recurrently from different populations of the parental species (polytopy), and it is also possible that a given taxonomic species may actually comprise several polyploid races, each originating from different progenitor species (polyphyly). To unravel the taxonomic complexity of polyploid Draba in the Nordic area, we investigated three of the most morphologically variable species and their possible progenitors using enzyme electrophoresis and restriction site analysis of chloroplast DNA (cpDNA) and nuclear ribosomal RNA genes (rDNA): D. norvegica (6x), D. lactea (6x), and D. corymbosa (16x). Electrophoretic analyses of progeny showed high levels of fixed heterozygosity in all three polyploids, demonstrating that all are genetic alloploids. Electrophoretic and rDNA data indicate that polytopic and/or polyphyletic origins have contributed to the complexity of these polyploids. However, a lack of cpDNA variation among the species limited the usefulness of this molecule for analysis of polyploid origins. The considerable electrophoretic variation observed in D. norvegica necessitates a minimum of three and probably 13 independent origins. Electrophoretic and rDNA data suggest that D. lactea and D. corymbosa are polyphyletic polyploids. Crossing data also support that D. corymbosa is polyphyletic. Given the widespread geographic distributions of these species and their possible progenitors, and that the populations analyzed represent only a small fraction of their geographic distributions, it is likely that these species have formed numerous times in different areas. As more molecular analyses of polyploids are completed, the data continue to suggest that multiple origins of polyploids are the rule rather than the exception.     

Doctors' retainer scheme in Scotland: time for change?

OBJECTIVES: To describe the present doctors'' retainer scheme in Scotland and ascertain the need for change. DESIGN: Semistructured postal questionnaires to current and past members of the doctors'' retainer scheme and general practitioner employers. SETTING: Scotland, October to December 1994. SUBJECTS: 152/160 current and 104/124 former members responded together with 101/118 general practitioner employers. RESULTS: 93% of members currently working in general practice were either vocationally trained or had previously worked as principals. 84% of current members held postgraduate qualifications. 73% of former members had left the scheme within 4 years and 72% of current members had been with the scheme for 4 years or less. 66% of current members said that the scheme prevented them from leaving medicine. Both members and employers were dissatisfied with the current limit of two working sessions per week, 77% of employers wanting it increased. 61% of current members would not have joined the scheme if suitable part time work had been available and 46% of those would have preferred to work flexibly, up to 5 sessions per week. 52% of members do not receive BMA rates of pay and, of those, 46% work more than 3.5 hours per session. CONCLUSION: The scheme appears to be appreciated and would be more so if inconsistencies in pay and conditions were addressed. An increase in the permitted number of weekly sessions would enable these highly qualified doctors to maintain their skills and confidence.     

Patterns of plant visitation by nectar-feeding lizards

Geckos in the genus Hoplodactylus visit flowers to feed on nectar. I examined the patterns of flower visitation exhibited by two gecko species (H. maculatus and H. duvauceli) having access to two plant species: pohutukawa (Metrosideros excelsa: Myrtaceae) and flax (Phormium tenax: Agavaceae). Individual geckos were not observed to visit both plant species; individuals visiting flax tended to revisit the same plant. Geckos visiting pohutukawa were larger than those visiting flax and exhibited an early night peak in plant visitation, while lizards on flax displayed a more even pattern of activity throughout the night. On flax, geckos were more likely to be found on plants with a greater number of male flowers. Male flax flowers were of greater diameter than female flowers and produced nectar at higher rates and with greater concentrations of sugars. Experimental manipulation of pohutukawa nectar volumes suggested that the distribution of geckos is influenced by the pattern of nectar availability.     

GENETIC CONSTRAINTS ON MACROEVOLUTION: THE EVOLUTION OF HOST AFFILIATION IN THE LEAF BEETLE GENUS OPHRAELLA

We hypothesize that the evolution of an ecologically important character, the host associations of specialized phytophagous insects, has been influenced by limitations on genetic variation. Using as a historical framework a phylogenetic reconstruction of the history of host associations in the beetle genus Ophraella (Chrysomelidae), we have employed quantitative-genetic methods to screen four species for genetic variation in larval survival, oviposition (in one species only), and feeding responses to their congeners' host plants, in the Asteraceae. We here report results of studies of one species and evaluate the results from all four. Analysis of half-sib/full-sib families and of progenies of wild females of O. notulata, a specialist on Iva (Ambrosiinae), provided evidence of genetic variation in larval consumption of five of six test plants and in adult consumption of four of six. Larval mortality was complete on five plants; only on Ambrosia, a close relative of the natural host, was there appreciable, and genetically variable, survival. Oviposition on Ambrosia showed marginally significant evidence of genetic variation; a more distantly related plant elicited no oviposition at all. In compiling results from four Ophraella species, reported in this and two other papers, we found no evidence of genetic variation in 18 of 39 tests of feeding responses and 14 of 16 tests of larval survival on congeners' hosts. This result is consistent with the hypothesis that absence or paucity of genetic variation may constrain or at least bias the evolution of host associations. The lower incidence of genetic variation in survival than in feeding behavior may imply, according to recent models, that avoidance is a more common evolutionary response to novel plants than adaptation. The usually great disparity between mean performance on congeners' hosts and the species' natural hosts, and an almost complete lack of evidence for negative genetic correlations, argue against the likelihood that speciation has occurred by sympatric host shift. The presence versus apparent absence of genetic variation in consumption was correlated with the propinquity of relationship between the beetle species tested and the species that normally feeds on the test plant, suggesting that the history of host shifts in Ophraella has been guided in part by restrictions on genetic variation. It was also correlated with the propinquity of relationship between a test plant and the beetle's natural host. The contributions of plant relationships and insect relationships, themselves correlated in part, to the pattern of genetic variation, are not readily distinguishable, but together accord with phylogenetic evidence that these and other phytophagous insects adapt most readily to related plants. In this instance, therefore, the macroevolution of an ecologically important character appears to have been influenced by genetic constraints. We hypothesize that absence of the structural prerequisites for genetic variation in complex characters may affect genetic variation and the trajectory of evolution.     

The amphotropic murine leukemia virus receptor gene encodes a 71-kilodalton protein that is induced by phosphate depletion.

The amphotropic murine leukemia virus (MuLV) can infect cells from a number of mammals, including humans, via its specific receptor. Basic knowledge of amphotropic MuLV receptor expression is likely to be useful in the development and improvement of gene therapy protocols based on amphotropic-pseudotyped vectors. To investigate the expression of the human receptor for the amphotropic MuLV (GLVR-2, newly termed Pit2), we determined its mRNA levels in several cell lines and found them to vary significantly. Induction of increased levels of mRNA after removal of phosphate from the media was observed in two osteosarcoma cell lines. The increase in GLVR-2 mRNA resulted in a concomitant rise in the levels of a 71-kDa protein specifically recognized by affinity-purified antibodies against GLVR-2. Using these antibodies, we were able to confirm the intracellular topology of the large hydrophilic domain between the proposed sixth and seventh transmembrane domains of the GLVR-2 protein. This assignment is in agreement with the fourth extracellular loop being outside the cell, consistent with the proposal that the fourth extracellular loop of GLVR-2 contains the envelope binding site.     

Assembly of local communities: consequences of an optimal body size for the organization of competitively structured communities

Much empirical evidence suggests that there is an optimal body size for mammals and that this optimum is in the vicinity of l00g. This presumably reflects an underlying fitness function that is greatest at this mass. Here, I combine such a fitness function with an equilibrium model of competitive character displacement to assess the potential influence of a globally optimal body size in structuring local ecological communities. The model accurately predicts the range of body sizes and the average difference in size for species in communities of varying species richness. The model also predicts a uniform spacing of body sizes, rather than the gaps and clumps in the sizes of coexisting species observed in real communities. Alternative explanations for this phenomenon are discussed. The allometric relationships that result in a body size optimum subsume a large number of characteristics associated with the physiological, behavioral, demographic, and evolutionary dynamics of the species. Further integration of the underlying dynamics (e.g. individual energetics) of these relationships into all hierarchical levels of ecology will have to incorporate multiple interactive sites, spatial heterogeneity, and phylogenetic structure, but it has the potential to provide important discoveries into the means by which natural selection operates.